/***
StyleSheet for use when a translation requires any css style changes.
This StyleSheet can be used directly by languages such as Chinese, Japanese and Korean which need larger font sizes.
***/
/*{{{*/
body {font-size:0.8em;}
#sidebarOptions {font-size:1.05em;}
#sidebarOptions a {font-style:normal;}
#sidebarOptions .sliderPanel {font-size:0.95em;}
.subtitle {font-size:0.8em;}
.viewer table.listView {font-size:0.95em;}
/*}}}*/

To get started with this blank TiddlyWiki, you'll need to modify the following tiddlers:
* SiteTitle & SiteSubtitle: The title and subtitle of the site, as shown above (after saving, they will also appear in the browser title bar)
* MainMenu: The menu (usually on the left)
* DefaultTiddlers: Contains the names of the tiddlers that you want to appear when the TiddlyWiki is opened
You'll also need to enter your username for signing your edits: <<option txtUserName>>

! Introduction
The algorithm is inspired by the meristogram of Huffman & Bullock [Huffman DG & Bullock WL: ''Meristograms: graphical analysis of serial variation of proboscis hooks of //Echinorhynchus// (Acanthocephala)'' //Systematic Zoology// 1975, 24:333-345].
! Data
Hook length and base measurements are recorded from at least one longitudinal row per specimen (see [[How to Measure Hooks]]). To demonstrate the algorithm we have data from three specimens: 1-3.
[img[Profiles of three longitudinal rows of hooks.|images/3_hook_rows.png]]
! Standardization of hook positions
The number of hooks per longitudinal row is variable, both within and between specimens. In this example specimens 1 and 2 have the same number of hooks per row (9) and so each numbered hook (1:9) on one proboscis can be compared directly to the same numbered hook on the other proboscis. However, on proboscis 3 there are 11 hooks and therefore hooks 10 and 11 do not have an equivalent hook on the other two proboscides. Furthermore, hooks 1:9 on proboscis 3 are probably not from homologous regions of the proboscis to hooks 1:9 on proboscides 1 and 2. To resolve this issue we standardize the hook positions using Huffman & Bullock's method; the counted position number of each hook in a given row is multiplied by 100 and divided by n + 1, where n = the total number of hooks in the row and the constant 1 is a corrective factor for centering the data points in graphs. The figure below shows length measurements plotted against standardized hook position.
[img[Hook length plotted against standardized hook position.|images/hook_length_vs_std_pos.png]]
Homologous regions of the proboscis can now be compared across the three specimens. However, the '50% position' is the only site where individual hooks can be compared directly. If the data were entered into a matrix where rows were length measurements and columns were standardized hook positions, there would be many missing values. For example, at the 10, 20, 30, 40, 60, 70, 80 and 90 '% positions' there would be missing data for specimen 3. Such an incomplete data matrix is unsuitable for multivariate statistical analysis.
! Moving Average Routine
Huffman and Bullock used a moving average routine to smooth the curves in their meristogram. Here, their approach is adopted to generate variables (hook dimensions) which may be compared across all individuals in a collection of worms. The moving average routine is applied to the data from each row of hooks and considers a user-defined segment of the percent-position axis for each measurement (length and base). The minimum size (m) for the moving average segment is calculated as:
m=ceiling((100/h+1)+1)
where h is the smallest number of hooks per longitudinal row recorded for the collection of worms. In the current example, the lowest number of hooks per row is 9 and so the minimum segment size is 11. If the size of the moving average segment was set below this value, one of more segments would not contain any hooks and therefore missing values would be generated by the moving average routine.
The segment advances through the data from anterior to posterior in 1% increments. After each advance of the segment, the arithmetic mean for the length measurements and base measurements of all hooks which fall within the segment are calculated. Note that the moving average routine is applied to each row of hooks, generating a length profile and a base profile for each row. This is different to Huffman & Bullock's meristogram, where data from all worms in a collection are summarized, to generate a single pattern describing the entire collection. Hook length profiles (generated using a moving average segment size of 11%) for the three example hook rows are shown in the figure below.
[img[Proboscis profiles for 3 specimens.|images/3profiles.png]]
! Pattern Recognition
The next step in the algorithm is unsupervised pattern recognition, which attempts to discover natural groups of hook rows sharing similar length and base profiles. The first stage of the pattern recognition process is to perform a principal component analysis (PCA) on the log transformed data (both length and base measurements).
Pattern recognition aims to identify morphotypes, //i.e.// groups of worms with similar proboscis profiles.
!!! Principal Component Analysis
The profiles generated from the moving average routine form a high-dimensional data set of almost 200 observations per hook row. Principal component analysis (PCA) is used to transform this large number of usually correlated variables into a smaller number of uncorrelated variables called principal components (PCs). If the PCA is effective, most of the variation in the dataset will be described by the first two PCs. Plotting the scores for the first two PCs will then show similarities between individual hook rows (see figure below), while the PC loadings (not shown) indicate the relative importance of the original variables.
[img[Proboscis profiles for 3 specimens.|images/pca3.png]]
In the above plot, PC1 (the PC describing the largest amount of variation in the data) separates specimen 1 from the other 2 specimens.
!!! Cluster Analysis
Hierarchical cluster analysis (complete agglomeration method with Euclidean distances) is performed on the first two principal components (//i.e.// the PCs describing the majority of the variation in the data) to provide an alternative visualization of morphological similarity between specimens.
[img[Cluster dendrogram for 3 specimens.|images/dendrogram3.png]]

!R classes and functions
The script [[acanthocephalan_proboscis_profiler.R | downloads/acanthocephalan_proboscis_profiler.R]] provides a number of classes and functions, for more detail see:
[[R class]]
[[R function]]

!1 Preparation
If R isn't already installed on your machine, you can download it for free from the [[R project website|http://www.r-project.org]].
Running Acanthocephalan Proboscis Profiler from the CLI will be easy if you already have some experience with the R environment. Don't worry if you don't have any experience with R, you should still be able to follow this guide. However, if you are interested in learning more about R you will find many introductory tutorials [[here|http://cran.r-project.org/other-docs.html]]. Official manuals can be found [[here|http://cran.r-project.org/manuals.html]].
N.B. If you are unfamiliar with R and have access to a computer running Windows XP/Vista, you may find it easier to use the [[Graphical User Interface (GUI)|Graphical User Interface]].
!2 Start R
!!!Linux/Unix
At the command line type ''R''
//{{{
mw283@ubuntu:~$ R
R version 2.9.2 (2009-08-24)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
//}}}
!!!Mac OSX
Go to applications and double-click on the R icon. Alternatively, open a terminal window and type ''R''
[img[Mac OSX R Console|images/macosxRconsole.png]]
!!!Windows
''Start Menu'' -> ''All Programs'' -> ''R''
[img[Windows R Console|images/windowsRconsole.jpg]]
!3 Read in source code
The latest version of the program can be sourced directly from our website (this will ensure you get the most up-to-date version):
//{{{
> source("http://acanthocephala.sourceforge.net/downloads/acanthocephalan_proboscis_profiler.R")
//}}}
!4 Read in raw data
Use [[readHookMeasurements]] function to read in your own data file (see [[Input File Format]]) or one of our example data files:
//{{{
> echRaw <- readHookMeasurements("http://acanthocephala.sourceforge.net/downloads/Echinorhynchus_spp.csv", notes="Data from three Echinorhynchus species")
//}}}
This creates an object of class hookMeasurements. To get a summary of the raw data use:
//{{{
> summary(echRaw)
Hook Measurements Summary
Number of groups: 3
Total number of specimens: 54
Number of specimens per group:
group number of specimens
1 E. gadi A 4
2 E. gadi B 4
3 E. truttae 46
Notes:
Data from three Echinorhynchus species
//}}}
!5 Generate proboscis profiles
Use [[profileProboscides]] function:
//{{{
> echProfiles <- profileProboscides(echRaw)
//}}}
Using default settings, profileProboscides generates profiles using the smallest moving average interval that can be applied to the raw data. To find out what moving average interval was applied, use the [[movAvgSeg]] function:
//{{{
> movAvgSeg(echProfiles)
[1] 11
//}}}
For a summary of the profiles use:
//{{{
> summary(echProfiles)
Proboscis Profiles Summary
Moving Average Segment: 11
Number of groups: 3
Total number of specimens: 54
Number of specimens per group:
group number of specimens
1 E. gadi A 4
2 E. gadi B 4
3 E. truttae 46
Notes:
Data from three Echinorhynchus species
//}}}
!6 Principal Component Analysis
Perform principal component analysis (PCA) on proboscis profiles:
//{{{
> echPCA <- prcomp(allHookMetrics(echProfiles))
//}}}
echPCA is an object of class ''prcomp''
To see the amount of variation described by the first two principal components use:
//{{{
> summary(echPCA)$importance[1:3,1:2]
PC1 PC2
Standard deviation 1.517088 0.6849417
Proportion of Variance 0.668140 0.1361900
Cumulative Proportion 0.668140 0.8043300
//}}}
Plot the scores for the first two principal components using:
//{{{
> plot(echPCA$x)
//}}}
[img[PCA scores plot|images/cli_pca.png]]
To use a distinct colour and symbol for each group, use:
//{{{
> plotColours <- gsub("E. truttae", "red", (gsub("E. gadi B", "green", (gsub("E. gadi A", "blue",annotation(echProfiles)$group)))))
> plotSymbols <- as.numeric(gsub("E. truttae", 3, (gsub("E. gadi B", 2, (gsub("E. gadi A", 1,annotation(echProfiles)$group))))))
> plot(echPCA$x, col=plotColours, pch=plotSymbols)
> legend("bottomleft", as.character(unique(annotation(echProfiles)$group)), pch=c(1,2,3), col=c("blue", "green", "red"))
//}}}
[img[PCA scores plot - groups labeled|images/cli_pca2.png]]
Identify individual points (specimens) in the plot by running the following command and then left-clicking on the points in the plot:
//{{{
> identify(echPCA$x, labels=as.character(annotation(echProfiles)$specimen))
//}}}
[img[PCA scores plot - individual specimens identified|images/cli_pca3.png]]
Right-click on graphics device to end indentification.
!7 Cluster Analysis
Perform cluster analysis and display the result as a dendrogram:
//{{{
> dendrogram <- hclust(dist(echPCA$x[,1:2], method='euclidean'), method='complete')
> plot(dendrogram, labels = paste(annotation(echProfiles)$group, annotation(echProfiles)$specimen, sep=' - '), xlab='', sub='', ylab='Distance')
//}}}
[img[Cluster Dendrogram|images/cluster_dendrogram.png]]
!8 Plot Profiles
First use the [[proboscisProfilesDataFrame]] function to create a data frame of your proboscis profiles data:
//{{{
> echDF <- proboscisProfilesDataFrame(echProfiles)
//}}}
Plots of length and base profiles can then be created using:
//{{{
> plotColours <- gsub("E. truttae", "red", (gsub("E. gadi B", "green", (gsub("E. gadi A", "blue",echDF$group)))))
> plotSymbols <- as.numeric(gsub("E. truttae", 3, (gsub("E. gadi B", 2, (gsub("E. gadi A", 1,echDF$group))))))
> par(mfrow=c(2,1))
> plot(echDF$position, echDF$length, pch=plotSymbols, col=plotColours, ylim=c(2.9,4.5), main="Length Profiles", xlab="Position (%)", ylab=expression(paste('Log Length', ' ', '(',mu,m,')')))
> legend("bottom", as.character(unique(echDF$group)), pch=c(1,2,3), col=c("blue", "green", "red"))
> plot(echDF$position, echDF$base, pch=plotSymbols, col=plotColours, main="Base Profiles", xlab="Position (%)", ylab=expression(paste('Log Base', ' ', '(',mu,m,')')))
> legend("bottom", as.character(unique(echDF$group)), pch=c(1,2,3), col=c("blue", "green", "red"))
//}}}
[img[Length and Base Profile Plots|images/cli_profile_plots.png]]
!9 Write Profile Data to File
Proboscis profile data can be written to a comma-separated-value file which can then be read into other applications.
To export both length and base profiles use the [[writeAllHookMetrics]] function:
//{{{
> writeAllHookMetrics(echProfiles, "Echinorhynchus_spp_profiles.csv")
//}}}
To export length profiles only use the [[writeHookLengthProfiles]] function:
//{{{
> writeHookLengthProfiles(echProfiles, "Echinorhynchus_spp_length_profiles.csv")
//}}}
To export base profiles only use the [[writeHookBaseProfiles]] function:
//{{{
> writeHookBaseProfiles(echProfiles, "Echinorhynchus_spp_base_profiles.csv")
//}}}

Acanthocephalan Proboscis Profiler is developed by Matt Wayland.
E-mail: mwayland[at]users.sourceforge.net
The ''Sourceforge'' project page for this software can be found [[here|https://sourceforge.net/projects/acanthocephala/]].

!R source code
The [[R source code|downloads/acanthocephalan_proboscis_profiler.R]] is platform independent. The source code is used from the [[command line interface (CLI) |CLI Quick Start Guide]] of [[R|http://www.r-project.org/]]. If you don't already have R installed on your computer it can be downloaded from the [[R-project website|http://www.r-project.org/]].
[[Download R source code for Acanthocephalan Proboscis Profiler|downloads/acanthocephalan_proboscis_profiler.R]]
!Windows GUI (Graphical User Interface)
Please read the [[installation instructions |GUI Installation]] before launching the installer.
[[Install Acanthocephalan Proboscis Profiler GUI|install/setup.exe]]
Source code for the windows GUI is also available in the form of a [[Visual Studio Express|http://www.microsoft.com/express/]] project.
[[Download source for Acanthocephalan Proboscis Profiler GUI|https://sourceforge.net/projects/acanthocephala/files/]]
!Example datasets
If you don't yet have any data to analyse, you can try out Acanthocephalan Proboscis Profiler using these example datasets:
*[[Echinorhynchus spp. example data]]
*[[Echinorhynchus salmonis example data]]

!Description
Hook measurements from 36 female specimens of //Echinorhynchus salmonis// Müller, 1784 (Acanthocephala: Echinorhynchidae) from the Bothnian Bay, Baltic Sea. The acanthocephalans were collected from the sea spawning form of the whitefish //Coregonus lavaretus// L. and the smelt //Osmerus eperlanus// (L.) from the Bothnian Bay, northern Baltic Sea. For each specimen a row of hooks from the dorsal surface of the proboscis and a row of hooks from the ventral surface of the proboscis were measured. The specimens from which these data were collected are deposited in The Natural History Museum, London.
|!Host|!Number of specimens|!Voucher Specimens|
|//Coregonus lavaretus// L.|22|BMNH 2002.2.4.132-226|
|//Osmerus eperlanus// (L.)|14|BMNH 2002.2.4.227-263|
!Download
[[Echinorhynchus_salmonis.csv|downloads/Echinorhynchus_salmonis.csv]]
First column of spreadsheet ('specimen') is the accession number, //e.g.// d17.15
The first letter indicates if the data came from a dorsal row ('d') or a ventral row (v).
The number before the full stop indicates the host of the acanthocephalan, either //C. lavaretus// (5) or //O. eperlanus// (17).
The number after the full stop is the specimen number.
!More information
For a detailed description of the material, please see the following publication:
Wayland, M.T., Gibson, D.I. & Sommerville, C. (2004) //Echinorhynchus salmonis// Müller, 1784 (Acanthocephala: Echinorhynchidae) from the Bothnian Bay, Baltic Sea: morphological variability and radial asymmetry of proboscis hooks. //Systematic Parasitology//, ''58'':149-158. ([[download| http://www.springerlink.com/content/k8584611t1934583/]])

!Plot Dendrogram Dialog
This dialog box enables you to control how a dendrogram of the hook profile data is plotted.
[img[Plot Dendrogram Dialog|images/dendrogram_dialog.JPG]]
!!!Options
''Title'' - Title for graph (default is //Cluster Dendrogram//).
''Title Size'' - Magnification to be used for the graph title (default is 1)
''Leaf Label'' - There are three choices for the leaf labels:
#group name and specimen unique identifier
#specimen unique identifier only
#group name only
''Leaf Label Size'' - Magnification to be used for the leaf labels (default is 1)
''Y Axis Label'' - An optional label for the Y Axis of the graph (default is //Distance//)
''Axis Label Size'' - Magnification to be used for the axis label (default is 1)
!Dendrogram Window
The dendrogram is generated in an R graphics window:
[img[Dendrogram|images/dendrogram.JPG]]
This window can be resized. Other options are listed below.
!!!Save Graph to File
Select ''File'' -> ''Save as'' and then choose one of the following file types:
*Metafile
*Postscript
*PDF
*Png
*Bmp
*TIFF
*Jpeg
!!!Copy Graph to the Clipboard
Select ''File'' -> ''Copy to the clipboard'' and then choose one of these two options:
#as a bitmap
#as a metafile
!!!Print Graph
Select ''File'' -> ''Print''

!Plot Hook Metrics Dialog
This dialog box enables you to control how the hook profile data are plotted.
[img[Plot Hook Metrics Dialog|images/plot_hook_metrics_dialog.JPG]]
!!!Options
''Data'' - choose either //raw// (original hook measurements) or //profiles// (metrics generated by moving average routine).
''Measurement'' - Select hook metric to plot from:
*Length
*Base
''Title Size'' - Magnification to be used for the graph title (default is 1)
''Symbol Size'' - Magnification to be used for the graph symbols (default is 1)
''Axis Label Size'' - Magnification to be used for the axis labels (default is 1)
''Tic Label Size'' - Magnification to be used for the tic labels (default is 1)
''Legend'' - Position of legend; choose one of the following options:
*no legend
*bottomright
*bottom
*bottomleft
*left
*topleft
*top
*topright
*right
*center
''Legend Size'' - Magnification to be used for the legend (default is 1)
''Group Colour'' - Select a colour from the drop-down list for each group
''Group Symbol'' - Select a symbol from the drop-down list for each group
''Identify Points'' - Check this box if you would like to be able to identify points on the graph by clicking on them.
!Hook Metric Plot Window
The plot is generated in an R graphics window.
[img[Profile Plot|images/profile_plot.JPG]]
This window can be resized. Other options are listed below.
!!!Identify points
If you checked the //Identify Points// box (see above) you can identify which specimen a plotted point belongs to, simply by clicking on it. Once you have finished identifying points, select ''Stop'' -> ''Stop locator''; you will then be able to access the other menu options (see below).
!!!Save Graph to File
Select ''File'' -> ''Save as'' and then choose one of the following file types:
*Metafile
*Postscript
*PDF
*Png
*Bmp
*TIFF
*Jpeg
!!!Copy Graph to the Clipboard
Select ''File'' -> ''Copy to the clipboard'' and then choose one of these two options:
#as a bitmap
#as a metafile
!!!Print Graph
Select ''File'' -> ''Print''

!Plot Principal Component Analysis (PCA) Scores
A simple PCA is performed when the proboscides are profiled. This dialog box enables you to plot the PCA loadings. The loadings define the size of the contribution of each original variable (hook measurement) to the PCs.
[img[Plot PCA loadings dialog|images/plot_pca_loadings_dialog.JPG]]
!!!Options
''X-axis'' - Principal Component (PC) to plot on x-axis
''Y-axis'' - PC to plot on y-axis
''Title'' - An optional title for the graph
''Title Size'' - Magnification to be used for the graph title (default is 1)
''Symbol Size'' - Magnification to be used for the graph symbols (default is 1)
''Axis Label Size'' - Magnification to be used for the axis labels (default is 1)
''Tic Label Size'' - Magnification to be used for the tic labels (default is 1)
!PCA Loadings Plot Window
The plot is generated in an R graphics window.
[img[PCA Loadings Plot|images/pca_loadings_plot.JPG]]
This window can be resized. Other options are listed below.
!!!Identify points
You can identify which variable (hook measurement) a plotted point belongs to, simply by clicking on it. Once you have finished identifying points, select ''Stop'' -> ''Stop locator''; you will then be able to access the other menu options (see below).
!!!Save Graph to File
Select ''File'' -> ''Save as'' and then choose one of the following file types:
*Metafile
*Postscript
*PDF
*Png
*Bmp
*TIFF
*Jpeg
!!!Copy Graph to the Clipboard
Select ''File'' -> ''Copy to the clipboard'' and then choose one of these two options:
#as a bitmap
#as a metafile
!!!Print Graph
Select ''File'' -> ''Print''

!Plot Principal Component Analysis (PCA) Scores
A simple PCA is performed when the proboscides are profiled. This dialog box enables you to plot the PCA scores.
[img[Plot PCA dialog|images/pca_dialog.JPG]]
!!!Options
''X-axis'' - Principal Component (PC) to plot on x-axis
''Y-axis'' - PC to plot on y-axis
''Title'' - An optional title for the graph
''Title Size'' - Magnification to be used for the graph title (default is 1)
''Symbol Size'' - Magnification to be used for the graph symbols (default is 1)
''Axis Label Size'' - Magnification to be used for the axis labels (default is 1)
''Tic Label Size'' - Magnification to be used for the tic labels (default is 1)
''Legend'' - Position of legend; choose one of the following options:
*no legend
*bottomright
*bottom
*bottomleft
*left
*topleft
*top
*topright
*right
*center
''Legend Size'' - Magnification to be used for the legend (default is 1)
''Group Colour'' - Select a colour from the drop-down list for each group
''Group Symbol'' - Select a symbol from the drop-down list for each group
''Identify Points'' - Check this box if you would like to be able to identify points on the graph by clicking on them.
!PCA Scores Plot Window
The plot is generated in an R graphics window.
[img[PCA Scores Plot|images/pca_scores_plot.JPG]]
This window can be resized. Other options are listed below.
!!!Identify points
If you checked the //Identify Points// box (see above) you can identify which specimen a plotted point belongs to, simply by clicking on it. Once you have finished identifying points, select ''Stop'' -> ''Stop locator''; you will then be able to access the other menu options (see below).
!!!Save Graph to File
Select ''File'' -> ''Save as'' and then choose one of the following file types:
*Metafile
*Postscript
*PDF
*Png
*Bmp
*TIFF
*Jpeg
!!!Copy Graph to the Clipboard
Select ''File'' -> ''Copy to the clipboard'' and then choose one of these two options:
#as a bitmap
#as a metafile
!!!Print Graph
Select ''File'' -> ''Print''

[img[Raw Data Form|images/raw_data_form.JPG]]
!Summary
This form displays the raw data that have been imported into the application. Notice that in addition to the data in the original import file (i.e. specimen, group, hook, length and base) an additional variable has been generated:
{{{Position}}} - standardised position = position as counted from distal end of proboscis X 100 / n+1, where n = number of hooks in longitudinal row.
!Options
!!!Export Data
To export data to a comma separated value (CSV) file, select ''File'' -> ''Export Data''
You will be prompted to give a file name and a location to store the file.
!!!Edit
Data cannot be changed, but they can be selected and copied.
To select all data use either the menu options:
''Edit'' -> ''Select All''
or use keyboard shortcut:
''Ctrl + A''
To copy selected data to the clipboard use either the menu options:
''Edit'' -> ''Copy''
or use the keyboard shortcut:
''Ctrl + C''
!!!Graph
To plot the raw data click ''Graph''.
This will open the [[Plot Hook Metrics Dialog|GUI - Plot Hook Metrics]]

When the application starts you will be presented with this form:
[img[form 1|images/form1.JPG]]
Click the ''Browse'' button to select a file of hook measurements (see [[Input File Format]] for detail of the type of file required) and then click ''Next'' to load the data.

Once the raw data are loaded the following form will be displayed:
[img[form 2|images/form2.JPG]]
This form provides a summary of the raw data. Clicking the ''View raw data'' button will open the [[Raw Data Form]] which displays the raw data and enables you to plot them and/or export them if required.
To generate the proboscis profiles select an appropriate moving average interval (the default is the minimum that can be applied to the dataset) and then click ''Next''.
Click ''Back'' button if you want to go back to the start page to load a different file of raw data.

!Compatible operating systems
Acanthocephalan Proboscis Profiler GUI has been tested on Windows Vista and XP. It may also work on other Windows operating systems.
!Prerequisites
To be able to run the Acanthocephalan Proboscis Profiler GUI you need to have the following software installed on your computer:
*[[R|http://www.r-project.org/]]
*[[rscproxy|http://cran.r-project.org/web/packages/rscproxy/index.html]]
*[[DCOM|http://rcom.univie.ac.at/]]
[[R|http://www.r-project.org/]], [[rscproxy|http://cran.r-project.org/web/packages/rscproxy/index.html]] and [[DCOM|http://rcom.univie.ac.at/]] should be installed according to the following instructions (administrator privileges required):
#Download the latest version of [[R|http://www.r-project.org/]] and install accepting default options.
# A default installation of R provides two versions: 32bit (R i386) and 64bit (R x64). Acanthocephalan Proboscis profiler works with the 32bit version. Right click on either the start menu entry or desktop shortcut labelled "R i386" and select "Run as administrator" from the pop-up menu. When running R as an administrator, packages will be installed in the system library directory, rather than your user directory. The package rscproxy must be installed in the system library.
#Install rscproxy. You can do this using the packages menu or you may find it easier to run this command in the terminal: install.packages("rscproxy")
# Finally install DCOM which is available here: [[http://rcom.univie.ac.at/download/current/statconnDCOM3.6-0B3_Noncommercial.exe|http://rcom.univie.ac.at/download/current/statconnDCOM3.6-0B3_Noncommercial.exe]]
# Your computer is now ready to install the Acanthocephalan Proboscis Profiler GUI
!ClickOnce Installer
The Acanthocephalan Proboscis Profiler GUI is deployed using the [[ClickOnce|http://en.wikipedia.org/wiki/ClickOnce]] installer which does not require administrator privileges. The application is installed per-user rather than per-machine. Click following link to install:
[[INSTALL|install/setup.exe]]
!GUI Updates
If your computer is connected to the internet the Acanthocephalan Proboscis Profiler GUI will automatically check for updates. If a new version of the software is available, you will see the following prompt asking if you would like to upgrade.
[img[Update Available Dialog|images/update_available.JPG]]

!1 Install Application
See [[GUI Installation]]
!2 Run Application
Launch the application:
''Start Menu'' -> ''All Programs'' -> ''Acanthocephala'' -> ''Acanthocephalan Proboscis Profiler''
When the application starts you will be presented with this form:
[img[form 1|images/form1.JPG]]
Click the ''Browse'' button to select a file of hook measurements (see [[Input File Format]] for detail of the type of file required) and then click ''Next'' to load the data.
!3 Raw data loaded
Once the raw data are loaded the following form will be displayed:
[img[form 2|images/form2.JPG]]
This form provides a summary of the raw data. Clicking the ''View raw data'' button will open the [[Raw Data Form]] which displays the raw data and enables you to plot them if required.
To generate the proboscis profiles click ''Next''. The default value for the moving average interval is the minimum value that can be applied to the data. The default moving average interval works well for the data-sets tested, but you can choose a different value if you wish.
!4 Profiles
Once the profiles have been computed the main form for the application will open, along with a dendrogram displaying the results of the cluster analysis.
!!!Dendrogram
[img[Dendrogram|images/dendrogram.JPG]]
The appearance of the dendrogram can be customized, see [[GUI - Dendrogram]]
!!!Main Form
[img[Main Form|images/main_form.JPG]]
The main form displays both the raw and profile data. For more information on the menu options see [[GUI - MainForm]]

!Armature of the acanthocephalan proboscis
[img[SEM of acanthocephalan proboscis with one longitudinal row of hooks highlighted.|images/long_row_hooks.png]]
Hooks are arranged in longitudinal rows. One longitudinal row is highlighted in the image above. To create a 'proboscis profile' we need measurements from each of the hooks in at least one longitudinal row of hooks per specimen.
!Preparation of material
On removal from the host, acanthocephalans should be washed and relaxed in distilled water, then fixed in 70% ethanol. All acanthocephalans should be prepared for light microscopy using the same protocol. I recommend dehydrating the specimens in an alcohol series and then clearing and mounting them in lactophenol.
!Light microscopy
Select a longitudinal row in which all hooks are visible in profile.
[img[Line drawing of one longitudinal row of hooks in profile|images/brayi_hooks.png]]
!Measurements
From each hook in your selected row record two measurements: length (L) and base (B).
[img[Length and base measurements|images/hook_measurements.png]]
Hook measurements should be entered into a spreadsheet, see [[Input File Format]]

The input file for Acanthocephalan Proboscis Profiler should be a comma separated value (CSV) file with 5 columns: specimen, group, hook, length and base.
{{{specimen}}} - unique identifier for the specimen (or row of hooks if more than one row was measured per specimen)
{{{group}}} - name of group
{{{hook}}} - numerical position of hook in longitudinal row as counted from the distal end of the probocis
{{{length}}} - length of hook blade
{{{base}}} - width of hook base
For instructions on collecting data, see [[How to Measure Hooks]]
Data can be entered into your favourite spreadsheet program and saved as a comma separated value (CSV) file:
[img[spreadsheet of raw data|images/data_format.JPG]]
Example data files are available:
*[[Echinorhynchus spp. example data]]
*[[Echinorhynchus salmonis example data]]

[>img[SEM of proboscis of Echinorhynchus truttae|images/truttae.png]]
The phylum [[Acanthocephala|http://en.wikipedia.org/wiki/Acanthocephala]] is comprised of over a thousand described species of bilaterally symmetrical, dioecious, pseudocoelomate worms. They are characterized by the presence of a retractable proboscis armed with rows of recurved hooks which provides the means of attachment to the definitive host's gut wall. Acanthocephalans lack an alimentary canal and food is absorbed directly through the body wall from the host. Acanthocephalan development requires at least two hosts, an arthropod intermediate host and a vertebrate definitive host. All major groups of vertebrates are parasitized by the Acanthocephala, although infections of agnathan and elasmobranch fishes are rare.
The Acanthocephala are a relatively homogenous group, displaying a limited number of features which can provide useful taxonomic characters. Hook morphometrics are of key significance in the discrimination of closely related species of acanthocephalans. Subtle differences in proboscis armature are often the only morphological characteristics which will distinguish congeneric species. The hooks covering the acanthocephalan proboscis are not uniform in size and shape; a longitudinal row of hooks will typically show morphometric variation from apex to base and radial asymmetry of hooks is not uncommon.
Molecular studies are revealing a previously unrecognized diversity in this phylum. Several nominal species have been shown to represent complexes of morphologically cryptic biological species, making the analysis of ecological data and the search for unknown intermediate hosts problematical.The Acanthocephalan Proboscis Profiler was designed to detect morphological heterogeneity in collections of morphologically similar acanthocephalan worms based on the multivariate statistical analysis of proboscis hooks. The Acanthocephalan Proboscis Profiler identifies objective, natural groups in a collection of worms which may correspond to distinct biological species or populations. Initial analyses have shown that the acanthocephalan proboscis profiler can discriminate biological species of the //Echinorhynchus gadi// complex and differentiate between dorsal and ventral hook rows from the proboscis of //Echinorhynchus salmonis//.
The [[algorithm|Algorithm]] is inspired by the meristogram of Huffman & Bullock [Huffman DG & Bullock WL: Meristograms: graphical analysis of serial variation of proboscis hooks of //Echinorhynchus// (Acanthocephala) Systematic Zoology 1975, 24:333-345].

/***
|Name:|LessBackupsPlugin|
|Description:|Intelligently limit the number of backup files you create|
|Version:|3.0.1 ($Rev: 2320 $)|
|Date:|$Date: 2007-06-18 22:37:46 +1000 (Mon, 18 Jun 2007) $|
|Source:|http://mptw.tiddlyspot.com/#LessBackupsPlugin|
|Author:|Simon Baird|
|Email:|simon.baird@gmail.com|
|License:|http://mptw.tiddlyspot.com/#TheBSDLicense|
!!Description
You end up with just backup one per year, per month, per weekday, per hour, minute, and second. So total number won't exceed about 200 or so. Can be reduced by commenting out the seconds/minutes/hours line from modes array
!!Notes
Works in IE and Firefox only. Algorithm by Daniel Baird. IE specific code by by Saq Imtiaz.
***/
//{{{
var MINS = 60 * 1000;
var HOURS = 60 * MINS;
var DAYS = 24 * HOURS;
if (!config.lessBackups) {
config.lessBackups = {
// comment out the ones you don't want or set config.lessBackups.modes in your 'tweaks' plugin
modes: [
["YYYY", 365*DAYS], // one per year for ever
["MMM", 31*DAYS], // one per month
["ddd", 7*DAYS], // one per weekday
//["d0DD", 1*DAYS], // one per day of month
["h0hh", 24*HOURS], // one per hour
["m0mm", 1*HOURS], // one per minute
["s0ss", 1*MINS], // one per second
["latest",0] // always keep last version. (leave this).
]
};
}
window.getSpecialBackupPath = function(backupPath) {
var now = new Date();
var modes = config.lessBackups.modes;
for (var i=0;i<modes.length;i++) {
// the filename we will try
var specialBackupPath = backupPath.replace(/(\.)([0-9]+\.[0-9]+)(\.html)$/,
'$1'+now.formatString(modes[i][0]).toLowerCase()+'$3')
// open the file
try {
if (config.browser.isIE) {
var fsobject = new ActiveXObject("Scripting.FileSystemObject")
var fileExists = fsobject.FileExists(specialBackupPath);
if (fileExists) {
var fileObject = fsobject.GetFile(specialBackupPath);
var modDate = new Date(fileObject.DateLastModified).valueOf();
}
}
else {
netscape.security.PrivilegeManager.enablePrivilege("UniversalXPConnect");
var file = Components.classes["@mozilla.org/file/local;1"].createInstance(Components.interfaces.nsILocalFile);
file.initWithPath(specialBackupPath);
var fileExists = file.exists();
if (fileExists) {
var modDate = file.lastModifiedTime;
}
}
}
catch(e) {
// give up
return backupPath;
}
// expiry is used to tell if it's an 'old' one. Eg, if the month is June and there is a
// June file on disk that's more than an month old then it must be stale so overwrite
// note that "latest" should be always written because the expiration period is zero (see above)
var expiry = new Date(modDate + modes[i][1]);
if (!fileExists || now > expiry)
return specialBackupPath;
}
}
// hijack the core function
window.getBackupPath_mptw_orig = window.getBackupPath;
window.getBackupPath = function(localPath) {
return getSpecialBackupPath(getBackupPath_mptw_orig(localPath));
}
//}}}

//{{{
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The GNU General Public License is a free, copyleft license for
software and other kinds of works.
The licenses for most software and other practical works are designed
to take away your freedom to share and change the works. By contrast,
the GNU General Public License is intended to guarantee your freedom to
share and change all versions of a program--to make sure it remains free
software for all its users. We, the Free Software Foundation, use the
GNU General Public License for most of our software; it applies also to
any other work released this way by its authors. You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
them if you wish), that you receive source code or can get it if you
want it, that you can change the software or use pieces of it in new
free programs, and that you know you can do these things.
To protect your rights, we need to prevent others from denying you
these rights or asking you to surrender the rights. Therefore, you have
certain responsibilities if you distribute copies of the software, or if
you modify it: responsibilities to respect the freedom of others.
For example, if you distribute copies of such a program, whether
gratis or for a fee, you must pass on to the recipients the same
freedoms that you received. You must make sure that they, too, receive
or can get the source code. And you must show them these terms so they
know their rights.
Developers that use the GNU GPL protect your rights with two steps:
(1) assert copyright on the software, and (2) offer you this License
giving you legal permission to copy, distribute and/or modify it.
For the developers' and authors' protection, the GPL clearly explains
that there is no warranty for this free software. For both users' and
authors' sake, the GPL requires that modified versions be marked as
changed, so that their problems will not be attributed erroneously to
authors of previous versions.
Some devices are designed to deny users access to install or run
modified versions of the software inside them, although the manufacturer
can do so. This is fundamentally incompatible with the aim of
protecting users' freedom to change the software. The systematic
pattern of such abuse occurs in the area of products for individuals to
use, which is precisely where it is most unacceptable. Therefore, we
have designed this version of the GPL to prohibit the practice for those
products. If such problems arise substantially in other domains, we
stand ready to extend this provision to those domains in future versions
of the GPL, as needed to protect the freedom of users.
Finally, every program is threatened constantly by software patents.
States should not allow patents to restrict development and use of
software on general-purpose computers, but in those that do, we wish to
avoid the special danger that patents applied to a free program could
make it effectively proprietary. To prevent this, the GPL assures that
patents cannot be used to render the program non-free.
The precise terms and conditions for copying, distribution and
modification follow.
TERMS AND CONDITIONS
0. Definitions.
"This License" refers to version 3 of the GNU General Public License.
"Copyright" also means copyright-like laws that apply to other kinds of
works, such as semiconductor masks.
"The Program" refers to any copyrightable work licensed under this
License. Each licensee is addressed as "you". "Licensees" and
"recipients" may be individuals or organizations.
To "modify" a work means to copy from or adapt all or part of the work
in a fashion requiring copyright permission, other than the making of an
exact copy. The resulting work is called a "modified version" of the
earlier work or a work "based on" the earlier work.
A "covered work" means either the unmodified Program or a work based
on the Program.
To "propagate" a work means to do anything with it that, without
permission, would make you directly or secondarily liable for
infringement under applicable copyright law, except executing it on a
computer or modifying a private copy. Propagation includes copying,
distribution (with or without modification), making available to the
public, and in some countries other activities as well.
To "convey" a work means any kind of propagation that enables other
parties to make or receive copies. Mere interaction with a user through
a computer network, with no transfer of a copy, is not conveying.
An interactive user interface displays "Appropriate Legal Notices"
to the extent that it includes a convenient and prominently visible
feature that (1) displays an appropriate copyright notice, and (2)
tells the user that there is no warranty for the work (except to the
extent that warranties are provided), that licensees may convey the
work under this License, and how to view a copy of this License. If
the interface presents a list of user commands or options, such as a
menu, a prominent item in the list meets this criterion.
1. Source Code.
The "source code" for a work means the preferred form of the work
for making modifications to it. "Object code" means any non-source
form of a work.
A "Standard Interface" means an interface that either is an official
standard defined by a recognized standards body, or, in the case of
interfaces specified for a particular programming language, one that
is widely used among developers working in that language.
The "System Libraries" of an executable work include anything, other
than the work as a whole, that (a) is included in the normal form of
packaging a Major Component, but which is not part of that Major
Component, and (b) serves only to enable use of the work with that
Major Component, or to implement a Standard Interface for which an
implementation is available to the public in source code form. A
"Major Component", in this context, means a major essential component
(kernel, window system, and so on) of the specific operating system
(if any) on which the executable work runs, or a compiler used to
produce the work, or an object code interpreter used to run it.
The "Corresponding Source" for a work in object code form means all
the source code needed to generate, install, and (for an executable
work) run the object code and to modify the work, including scripts to
control those activities. However, it does not include the work's
System Libraries, or general-purpose tools or generally available free
programs which are used unmodified in performing those activities but
which are not part of the work. For example, Corresponding Source
includes interface definition files associated with source files for
the work, and the source code for shared libraries and dynamically
linked subprograms that the work is specifically designed to require,
such as by intimate data communication or control flow between those
subprograms and other parts of the work.
The Corresponding Source need not include anything that users
can regenerate automatically from other parts of the Corresponding
Source.
The Corresponding Source for a work in source code form is that
same work.
2. Basic Permissions.
All rights granted under this License are granted for the term of
copyright on the Program, and are irrevocable provided the stated
conditions are met. This License explicitly affirms your unlimited
permission to run the unmodified Program. The output from running a
covered work is covered by this License only if the output, given its
content, constitutes a covered work. This License acknowledges your
rights of fair use or other equivalent, as provided by copyright law.
You may make, run and propagate covered works that you do not
convey, without conditions so long as your license otherwise remains
in force. You may convey covered works to others for the sole purpose
of having them make modifications exclusively for you, or provide you
with facilities for running those works, provided that you comply with
the terms of this License in conveying all material for which you do
not control copyright. Those thus making or running the covered works
for you must do so exclusively on your behalf, under your direction
and control, on terms that prohibit them from making any copies of
your copyrighted material outside their relationship with you.
Conveying under any other circumstances is permitted solely under
the conditions stated below. Sublicensing is not allowed; section 10
makes it unnecessary.
3. Protecting Users' Legal Rights From Anti-Circumvention Law.
No covered work shall be deemed part of an effective technological
measure under any applicable law fulfilling obligations under article
11 of the WIPO copyright treaty adopted on 20 December 1996, or
similar laws prohibiting or restricting circumvention of such
measures.
When you convey a covered work, you waive any legal power to forbid
circumvention of technological measures to the extent such circumvention
is effected by exercising rights under this License with respect to
the covered work, and you disclaim any intention to limit operation or
modification of the work as a means of enforcing, against the work's
users, your or third parties' legal rights to forbid circumvention of
technological measures.
4. Conveying Verbatim Copies.
You may convey verbatim copies of the Program's source code as you
receive it, in any medium, provided that you conspicuously and
appropriately publish on each copy an appropriate copyright notice;
keep intact all notices stating that this License and any
non-permissive terms added in accord with section 7 apply to the code;
keep intact all notices of the absence of any warranty; and give all
recipients a copy of this License along with the Program.
You may charge any price or no price for each copy that you convey,
and you may offer support or warranty protection for a fee.
5. Conveying Modified Source Versions.
You may convey a work based on the Program, or the modifications to
produce it from the Program, in the form of source code under the
terms of section 4, provided that you also meet all of these conditions:
a) The work must carry prominent notices stating that you modified
it, and giving a relevant date.
b) The work must carry prominent notices stating that it is
released under this License and any conditions added under section
7. This requirement modifies the requirement in section 4 to
"keep intact all notices".
c) You must license the entire work, as a whole, under this
License to anyone who comes into possession of a copy. This
License will therefore apply, along with any applicable section 7
additional terms, to the whole of the work, and all its parts,
regardless of how they are packaged. This License gives no
permission to license the work in any other way, but it does not
invalidate such permission if you have separately received it.
d) If the work has interactive user interfaces, each must display
Appropriate Legal Notices; however, if the Program has interactive
interfaces that do not display Appropriate Legal Notices, your
work need not make them do so.
A compilation of a covered work with other separate and independent
works, which are not by their nature extensions of the covered work,
and which are not combined with it such as to form a larger program,
in or on a volume of a storage or distribution medium, is called an
"aggregate" if the compilation and its resulting copyright are not
used to limit the access or legal rights of the compilation's users
beyond what the individual works permit. Inclusion of a covered work
in an aggregate does not cause this License to apply to the other
parts of the aggregate.
6. Conveying Non-Source Forms.
You may convey a covered work in object code form under the terms
of sections 4 and 5, provided that you also convey the
machine-readable Corresponding Source under the terms of this License,
in one of these ways:
a) Convey the object code in, or embodied in, a physical product
(including a physical distribution medium), accompanied by the
Corresponding Source fixed on a durable physical medium
customarily used for software interchange.
b) Convey the object code in, or embodied in, a physical product
(including a physical distribution medium), accompanied by a
written offer, valid for at least three years and valid for as
long as you offer spare parts or customer support for that product
model, to give anyone who possesses the object code either (1) a
copy of the Corresponding Source for all the software in the
product that is covered by this License, on a durable physical
medium customarily used for software interchange, for a price no
more than your reasonable cost of physically performing this
conveying of source, or (2) access to copy the
Corresponding Source from a network server at no charge.
c) Convey individual copies of the object code with a copy of the
written offer to provide the Corresponding Source. This
alternative is allowed only occasionally and noncommercially, and
only if you received the object code with such an offer, in accord
with subsection 6b.
d) Convey the object code by offering access from a designated
place (gratis or for a charge), and offer equivalent access to the
Corresponding Source in the same way through the same place at no
further charge. You need not require recipients to copy the
Corresponding Source along with the object code. If the place to
copy the object code is a network server, the Corresponding Source
may be on a different server (operated by you or a third party)
that supports equivalent copying facilities, provided you maintain
clear directions next to the object code saying where to find the
Corresponding Source. Regardless of what server hosts the
Corresponding Source, you remain obligated to ensure that it is
available for as long as needed to satisfy these requirements.
e) Convey the object code using peer-to-peer transmission, provided
you inform other peers where the object code and Corresponding
Source of the work are being offered to the general public at no
charge under subsection 6d.
A separable portion of the object code, whose source code is excluded
from the Corresponding Source as a System Library, need not be
included in conveying the object code work.
A "User Product" is either (1) a "consumer product", which means any
tangible personal property which is normally used for personal, family,
or household purposes, or (2) anything designed or sold for incorporation
into a dwelling. In determining whether a product is a consumer product,
doubtful cases shall be resolved in favor of coverage. For a particular
product received by a particular user, "normally used" refers to a
typical or common use of that class of product, regardless of the status
of the particular user or of the way in which the particular user
actually uses, or expects or is expected to use, the product. A product
is a consumer product regardless of whether the product has substantial
commercial, industrial or non-consumer uses, unless such uses represent
the only significant mode of use of the product.
"Installation Information" for a User Product means any methods,
procedures, authorization keys, or other information required to install
and execute modified versions of a covered work in that User Product from
a modified version of its Corresponding Source. The information must
suffice to ensure that the continued functioning of the modified object
code is in no case prevented or interfered with solely because
modification has been made.
If you convey an object code work under this section in, or with, or
specifically for use in, a User Product, and the conveying occurs as
part of a transaction in which the right of possession and use of the
User Product is transferred to the recipient in perpetuity or for a
fixed term (regardless of how the transaction is characterized), the
Corresponding Source conveyed under this section must be accompanied
by the Installation Information. But this requirement does not apply
if neither you nor any third party retains the ability to install
modified object code on the User Product (for example, the work has
been installed in ROM).
The requirement to provide Installation Information does not include a
requirement to continue to provide support service, warranty, or updates
for a work that has been modified or installed by the recipient, or for
the User Product in which it has been modified or installed. Access to a
network may be denied when the modification itself materially and
adversely affects the operation of the network or violates the rules and
protocols for communication across the network.
Corresponding Source conveyed, and Installation Information provided,
in accord with this section must be in a format that is publicly
documented (and with an implementation available to the public in
source code form), and must require no special password or key for
unpacking, reading or copying.
7. Additional Terms.
"Additional permissions" are terms that supplement the terms of this
License by making exceptions from one or more of its conditions.
Additional permissions that are applicable to the entire Program shall
be treated as though they were included in this License, to the extent
that they are valid under applicable law. If additional permissions
apply only to part of the Program, that part may be used separately
under those permissions, but the entire Program remains governed by
this License without regard to the additional permissions.
When you convey a copy of a covered work, you may at your option
remove any additional permissions from that copy, or from any part of
it. (Additional permissions may be written to require their own
removal in certain cases when you modify the work.) You may place
additional permissions on material, added by you to a covered work,
for which you have or can give appropriate copyright permission.
Notwithstanding any other provision of this License, for material you
add to a covered work, you may (if authorized by the copyright holders of
that material) supplement the terms of this License with terms:
a) Disclaiming warranty or limiting liability differently from the
terms of sections 15 and 16 of this License; or
b) Requiring preservation of specified reasonable legal notices or
author attributions in that material or in the Appropriate Legal
Notices displayed by works containing it; or
c) Prohibiting misrepresentation of the origin of that material, or
requiring that modified versions of such material be marked in
reasonable ways as different from the original version; or
d) Limiting the use for publicity purposes of names of licensors or
authors of the material; or
e) Declining to grant rights under trademark law for use of some
trade names, trademarks, or service marks; or
f) Requiring indemnification of licensors and authors of that
material by anyone who conveys the material (or modified versions of
it) with contractual assumptions of liability to the recipient, for
any liability that these contractual assumptions directly impose on
those licensors and authors.
All other non-permissive additional terms are considered "further
restrictions" within the meaning of section 10. If the Program as you
received it, or any part of it, contains a notice stating that it is
governed by this License along with a term that is a further
restriction, you may remove that term. If a license document contains
a further restriction but permits relicensing or conveying under this
License, you may add to a covered work material governed by the terms
of that license document, provided that the further restriction does
not survive such relicensing or conveying.
If you add terms to a covered work in accord with this section, you
must place, in the relevant source files, a statement of the
additional terms that apply to those files, or a notice indicating
where to find the applicable terms.
Additional terms, permissive or non-permissive, may be stated in the
form of a separately written license, or stated as exceptions;
the above requirements apply either way.
8. Termination.
You may not propagate or modify a covered work except as expressly
provided under this License. Any attempt otherwise to propagate or
modify it is void, and will automatically terminate your rights under
this License (including any patent licenses granted under the third
paragraph of section 11).
However, if you cease all violation of this License, then your
license from a particular copyright holder is reinstated (a)
provisionally, unless and until the copyright holder explicitly and
finally terminates your license, and (b) permanently, if the copyright
holder fails to notify you of the violation by some reasonable means
prior to 60 days after the cessation.
Moreover, your license from a particular copyright holder is
reinstated permanently if the copyright holder notifies you of the
violation by some reasonable means, this is the first time you have
received notice of violation of this License (for any work) from that
copyright holder, and you cure the violation prior to 30 days after
your receipt of the notice.
Termination of your rights under this section does not terminate the
licenses of parties who have received copies or rights from you under
this License. If your rights have been terminated and not permanently
reinstated, you do not qualify to receive new licenses for the same
material under section 10.
9. Acceptance Not Required for Having Copies.
You are not required to accept this License in order to receive or
run a copy of the Program. Ancillary propagation of a covered work
occurring solely as a consequence of using peer-to-peer transmission
to receive a copy likewise does not require acceptance. However,
nothing other than this License grants you permission to propagate or
modify any covered work. These actions infringe copyright if you do
not accept this License. Therefore, by modifying or propagating a
covered work, you indicate your acceptance of this License to do so.
10. Automatic Licensing of Downstream Recipients.
Each time you convey a covered work, the recipient automatically
receives a license from the original licensors, to run, modify and
propagate that work, subject to this License. You are not responsible
for enforcing compliance by third parties with this License.
An "entity transaction" is a transaction transferring control of an
organization, or substantially all assets of one, or subdividing an
organization, or merging organizations. If propagation of a covered
work results from an entity transaction, each party to that
transaction who receives a copy of the work also receives whatever
licenses to the work the party's predecessor in interest had or could
give under the previous paragraph, plus a right to possession of the
Corresponding Source of the work from the predecessor in interest, if
the predecessor has it or can get it with reasonable efforts.
You may not impose any further restrictions on the exercise of the
rights granted or affirmed under this License. For example, you may
not impose a license fee, royalty, or other charge for exercise of
rights granted under this License, and you may not initiate litigation
(including a cross-claim or counterclaim in a lawsuit) alleging that
any patent claim is infringed by making, using, selling, offering for
sale, or importing the Program or any portion of it.
11. Patents.
A "contributor" is a copyright holder who authorizes use under this
License of the Program or a work on which the Program is based. The
work thus licensed is called the contributor's "contributor version".
A contributor's "essential patent claims" are all patent claims
owned or controlled by the contributor, whether already acquired or
hereafter acquired, that would be infringed by some manner, permitted
by this License, of making, using, or selling its contributor version,
but do not include claims that would be infringed only as a
consequence of further modification of the contributor version. For
purposes of this definition, "control" includes the right to grant
patent sublicenses in a manner consistent with the requirements of
this License.
Each contributor grants you a non-exclusive, worldwide, royalty-free
patent license under the contributor's essential patent claims, to
make, use, sell, offer for sale, import and otherwise run, modify and
propagate the contents of its contributor version.
In the following three paragraphs, a "patent license" is any express
agreement or commitment, however denominated, not to enforce a patent
(such as an express permission to practice a patent or covenant not to
sue for patent infringement). To "grant" such a patent license to a
party means to make such an agreement or commitment not to enforce a
patent against the party.
If you convey a covered work, knowingly relying on a patent license,
and the Corresponding Source of the work is not available for anyone
to copy, free of charge and under the terms of this License, through a
publicly available network server or other readily accessible means,
then you must either (1) cause the Corresponding Source to be so
available, or (2) arrange to deprive yourself of the benefit of the
patent license for this particular work, or (3) arrange, in a manner
consistent with the requirements of this License, to extend the patent
license to downstream recipients. "Knowingly relying" means you have
actual knowledge that, but for the patent license, your conveying the
covered work in a country, or your recipient's use of the covered work
in a country, would infringe one or more identifiable patents in that
country that you have reason to believe are valid.
If, pursuant to or in connection with a single transaction or
arrangement, you convey, or propagate by procuring conveyance of, a
covered work, and grant a patent license to some of the parties
receiving the covered work authorizing them to use, propagate, modify
or convey a specific copy of the covered work, then the patent license
you grant is automatically extended to all recipients of the covered
work and works based on it.
A patent license is "discriminatory" if it does not include within
the scope of its coverage, prohibits the exercise of, or is
conditioned on the non-exercise of one or more of the rights that are
specifically granted under this License. You may not convey a covered
work if you are a party to an arrangement with a third party that is
in the business of distributing software, under which you make payment
to the third party based on the extent of your activity of conveying
the work, and under which the third party grants, to any of the
parties who would receive the covered work from you, a discriminatory
patent license (a) in connection with copies of the covered work
conveyed by you (or copies made from those copies), or (b) primarily
for and in connection with specific products or compilations that
contain the covered work, unless you entered into that arrangement,
or that patent license was granted, prior to 28 March 2007.
Nothing in this License shall be construed as excluding or limiting
any implied license or other defenses to infringement that may
otherwise be available to you under applicable patent law.
12. No Surrender of Others' Freedom.
If conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License. If you cannot convey a
covered work so as to satisfy simultaneously your obligations under this
License and any other pertinent obligations, then as a consequence you may
not convey it at all. For example, if you agree to terms that obligate you
to collect a royalty for further conveying from those to whom you convey
the Program, the only way you could satisfy both those terms and this
License would be to refrain entirely from conveying the Program.
13. Use with the GNU Affero General Public License.
Notwithstanding any other provision of this License, you have
permission to link or combine any covered work with a work licensed
under version 3 of the GNU Affero General Public License into a single
combined work, and to convey the resulting work. The terms of this
License will continue to apply to the part which is the covered work,
but the special requirements of the GNU Affero General Public License,
section 13, concerning interaction through a network will apply to the
combination as such.
14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of
the GNU General Public License from time to time. Such new versions will
be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.
Each version is given a distinguishing version number. If the
Program specifies that a certain numbered version of the GNU General
Public License "or any later version" applies to it, you have the
option of following the terms and conditions either of that numbered
version or of any later version published by the Free Software
Foundation. If the Program does not specify a version number of the
GNU General Public License, you may choose any version ever published
by the Free Software Foundation.
If the Program specifies that a proxy can decide which future
versions of the GNU General Public License can be used, that proxy's
public statement of acceptance of a version permanently authorizes you
to choose that version for the Program.
Later license versions may give you additional or different
permissions. However, no additional obligations are imposed on any
author or copyright holder as a result of your choosing to follow a
later version.
15. Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
16. Limitation of Liability.
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
<program> Copyright (C) <year> <name of author>
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<http://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<http://www.gnu.org/philosophy/why-not-lgpl.html>.
//}}}

MPTW is a distribution or edition of TiddlyWiki that includes a standard TiddlyWiki core packaged with some plugins designed to improve usability and provide a better way to organise your information. For more information see http://mptw.tiddlyspot.com/.

For upgrading. See [[ImportTiddlers]].
URL: http://mptw.tiddlyspot.com/upgrade.html

/***
|Description:|A place to put your config tweaks so they aren't overwritten when you upgrade MPTW|
See http://www.tiddlywiki.org/wiki/Configuration_Options for other options you can set. In some cases where there are clashes with other plugins it might help to rename this to zzMptwUserConfigPlugin so it gets executed last.
***/
//{{{
// example: set your preferred date format
//config.mptwDateFormat = 'MM/0DD/YY';
//config.mptwJournalFormat = 'Journal MM/0DD/YY';
// example: set the theme you want to start with
//config.options.txtTheme = 'MptwRoundTheme';
// example: switch off autosave, switch on backups and set a backup folder
//config.options.chkSaveBackups = true;
//config.options.chkAutoSave = false;
//config.options.txtBackupFolder = 'backups';
// uncomment to disable 'new means new' functionality for the new journal macro
//config.newMeansNewForJournalsToo = false;
//}}}

!Description
Extracts all hook metrics from a [[proboscisProfiles]] object.
!Usage
//{{{
allHookMetrics(proboscisProfiles)
//}}}
!Arguments
{{{proboscisProfiles}}} - an object of class [[proboscisProfiles]]
!Value
A matrix where rows are specimens and columns are moving average centres (%) for each metric: l (length) and b (base).

!Description
Extracts annotation from a [[proboscisProfiles]] object.
!Usage
//{{{
annotation(proboscisProfiles)
//}}}
!Arguments
{{{proboscisProfiles}}} - an object of class [[proboscisProfiles]]
!Value
A data.frame with three columns: specimen, group and numberHooks.

!Description
Function for returning the number of hooks per longitudinal row for each specimen in a [[hookMeasurements]] object.
!Usage
//{{{
hooksPerRow(object)
//}}}
!Arguments
{{{object}}} - an object of class [[hookMeasurements]]
!Value
A data.frame with three columns: specimen, group and numberHooks

!Description
Function for calculating the minimum moving average interval that can be applied to a [[hookMeasurements]] object using the [[profileProboscides]] function.
!Usage
//{{{
minMovAvgSeg(hookMeasurements)
//}}}
!Arguments
{{{hookMeasurements}}} - an object of class [[hookMeasurements]]
!Value
An object of class numeric

!Description
Extracts notes (if they exist) from a hookMeasurements or proboscisProfiles object.
!Usage
notes(x)
!Arguments
{{{x}}} - an object of class [[hookMeasurements]] or [[proboscisProfiles]]
!Value
An object of class character

!Description
Puts data in a [[proboscisProfiles]] object into a data.frame, which is an easier format for plotting profiles, etc.
!Usage
//{{{
proboscisProfilesDataFrame(x)
//}}}
!Arguments
{{{x}}} - an object of class [[proboscisProfiles]]
!Value
An object of class data.frame with the following columns: "specimen", "group", "position", "length" and "base".

!Description
Function for generating proboscis profiles from data stored in a [[hookMeasurements]] object.
!Usage
//{{{
profileProboscides(hookMeasurements, movAvgSeg, ln)
//}}}
!Arguments
{{{hookMeasurements}}} - an object of class [[hookMeasurements]]
{{{movAvgSeg}}} - optional numeric value for size of moving average interval (defaults to minimum moving average interval that can be applied to the dataset).
{{{ln}}} - a logical value (TRUE or FALSE) to indicate if output hook metrics should be transformed to natural logarithms (default is TRUE).
!Value
An object of class [[proboscisProfiles]]

!Description
Function to display objects of class [[hookMeasurementsSummary]]. Equivalent to [[print.hookMeasurementsSummary]]. The show function is used for automatic printing of objects.
!Usage
//{{{
show(object)
//}}}
or
//{{{
show.hookMeasurementsSummary(object)
//}}}
!Arguments
{{{object}}} - an object of class [[hookMeasurementsSummary]]

!Description
Function to display objects of class [[proboscisProfilesSummary]]. Equivalent to [[print.proboscisProfilesSummary]]. The show function is used for automatic printing of objects.
!Usage
//{{{
show(object)
//}}}
or
//{{{
show.proboscisProfilesSummary(object)
//}}}
!Arguments
{{{object}}} - an object of class [[proboscisProfilesSummary]]